[gmx-users] Re: Fluctuations in NVT and NPT resulting plots

Justin Lemkul jalemkul at vt.edu
Sun Oct 21 16:22:54 CEST 2012

On 10/21/12 8:21 AM, Ali Alizadeh wrote:
> Dear Justin
> It is true that we can not  get profile volume vs. time(only nvt
> step), but after that we performed production md, we can
> illustrate profile density and volume profile vs. time. However we
> cannot get constant volume!
> Do I mistake? If it is possible , You can explain more about that fluctuation?

If the ensemble is NPT during the production run, then the box volume is not 
constant.  Pressure is constant (on average) and thus the box vectors will 
fluctuate in response to the pressure coupling algorithm scaling the vectors. 
If you are unclear on how this works, then please refer to the primary 
literature for the pressure coupling algorithm you are using to understand what 
it is doing.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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